High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe-Why trends of virus evolution are more difficult to predict

Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology, and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species. After the two consecutive and devastating epidemic waves in Europe in 2020-2021 and 2021-2022, with the second one recognized as one of the largest epidemics recorded so far, this clade has begun to circulate endemically in European wild bird populations. This study used the complete genomes of 1,956 European HPAI A(H5Nx) viruses to investigate the virus evolution during this varying epidemiological outline. We investigated the spatiotemporal patterns of A(H5Nx) virus diffusion to/from and within Europe during the 2020-2021 and 2021-2022 epidemic waves, providing evidence of ongoing changes in transmission dynamics and disease epidemiology. We demonstrated the high genetic diversity of the circulating viruses, which have undergone frequent reassortment events, providing for the first time a complete overview and a proposed nomenclature of the multiple genotypes circulating in Europe in 2020-2022. We described the emergence of a new genotype with gull adapted genes, which offered the virus the opportunity to occupy new ecological niches, driving the disease endemicity in the European wild bird population. The high propensity of the virus for reassortment, its jumps to a progressively wider number of host species, including mammals, and the rapid acquisition of adaptive mutations make the trend of virus evolution and spread difficult to predict in this unfailing evolving scenario.

Wastewater-based prediction of COVID-19 cases using a random forest algorithm with strain prevalence data: A case study of five municipalities in Latvia

Wastewater-based epidemiology (WBE) is a rapid and cost-effective method that can detect SARS-CoV-2 genomic components in wastewater and can provide an early warning for possible COVID-19 outbreaks up to one or two weeks in advance. However, the quantitative relationship between the intensity of the epidemic and the possible progression of the pandemic is still unclear, necessitating further research. This study investigates the use of WBE to rapidly monitor the SARS-CoV-2 virus from five municipal wastewater treatment plants in Latvia and forecast cumulative COVID-19 cases two weeks in advance. For this purpose, a real-time quantitative PCR approach was used to monitor the SARS-CoV-2 nucleocapsid 1 (N1), nucleocapsid 2 (N2), and E genes in municipal wastewater. The RNA signals in the wastewater were compared to the reported COVID-19 cases, and the strain prevalence data of the SARS-CoV-2 virus were identified by targeted sequencing of receptor binding domain (RBD) and furin cleavage site (FCS) regions employing next-generation sequencing technology. The model methodology for a linear model and a random forest was designed and carried out to ascertain the correlation between the cumulative cases, strain prevalence data, and RNA concentration in the wastewater to predict the COVID-19 outbreak and its scale. Additionally, the factors that impact the model prediction accuracy for COVID-19 were investigated and compared between linear and random forest models. The results of cross-validated model metrics showed that the random forest model is more effective in predicting the cumulative COVID-19 cases two weeks in advance when strain prevalence data are included. The results from this research help inform WBE and public health recommendations by providing valuable insights into the impact of environmental exposures on health outcomes.

Do Seropositive Wild Boars Pose a Risk for the Spread of African Swine Fever? Analysis of Field Data from Latvia and Lithuania

In 2020, ASF occurred in wild boars throughout Latvia and Lithuania, and more than 21,500 animals were hunted and tested for the presence of the virus genome and antibodies in the framework of routine disease surveillance. The aim of our study was to re-examine hunted wild boars that tested positive for the antibodies and negative for the virus genome in the blood (n = 244) and to see if the virus genome can still be found in the bone marrow, as an indicator of virus persistence in the animal. Via this approach, we intended to answer the question of whether seropositive animals play a role in the spread of the disease. In total, 2 seropositive animals out of 244 were found to be positive for the ASF virus genome in the bone marrow. The results indicate that seropositive animals, which theoretically could also be virus shedders, can hardly be found in the field and thus do not play an epidemiological role regarding virus perpetuation, at least not in the wild boar populations we studied.

A multi gene-approach genotyping method identifies 24 genetic clusters within the genotype II-European African swine fever viruses circulating from 2007 to 2022

Introduction

African swine fever (ASF) is a contagious viral disease of pigs and wild boar that poses a major threat to the global swine industry. The genotype II African swine fever virus (ASFV) entered the European Union (EU) in 2014 and since then fourteen countries have been affected, Italy and North Macedonia being the last in 2022. While whole genome sequencing remains the gold standard for the identification of new genetic markers, sequencing of multiple loci with significant variations could be used as a rapid and cost-effective alternative to track outbreaks and study disease evolution in endemic areas.

Materials and methods

To further our understanding of the epidemiology and spread of ASFV in Europe, 382 isolates collected during 2007 to 2022 were sequenced. The study was initially performed by sequencing the central variable region (CVR), the intergenic region (IGR) between the I73R and I329L genes and the O174L and K145R genes. For further discrimination, two new PCRs were designed to amplify the IGR between the 9R and 10R genes of the multigene family 505 (MGF505) and the IGR between the I329L and I215L genes. The sequences obtained were compared with genotype II isolates from Europe and Asia.

Results

The combination of the results obtained by sequencing these variable regions allowed to differentiate the European II-ASFV genotypes into 24 different groups. In addition, the SNP identified in the IGR I329L-I215L region, not previously described, grouped the viruses from North Macedonia that caused the 2022 outbreaks with viruses from Romania, Bulgaria, Serbia and Greece, differentiating from other genotype II isolates present in Europe and Asia. Furthermore, tandem repeat sequence (TRS) within the 9R-10R genes of the multigene family 505 (MGF505) revealed eight different variants circulating.

Discussion

These findings describe a new multi-gene approach sequencing method that can be used in routine genotyping to determine the origin of new introductions in ASF-free areas and track infection dynamics in endemic areas.